tbuckley/cabot-search huggingface dataset:
ANGI-01. INDUCIBLE CAS9 IN PATIENT-DERIVED CULTURES OF IDH WILDTYPE GLIOBLASTOMA WITH DISTINCT GROWTH CHARACTERISTICS
Authors: Soumi Kundu, Irem Yildirim, Faidra Voukelatou, Rebecka Stockgard, Cecilia Krona, Sven Nelander
Journal: Neuro-Oncology (2023)

Abstract To identify new treatment opportunities for IDH wildtype glioblastoma, it is essential to establish robust methods to evaluate candidate genes in patient-derived cells. Here, we report initiative to establish large-scale candidate gene evaluation by CRISPR-Cas9 using well characterized cells from the Uppsala Human Glioma Cell Culture biobank. Previously, we have characterized fully the HGCC cultures (n = 100) in terms of multi-omics, and by systematic injection as patient-derived orthotopic xenografts. Here, we report a procedure to introduce doxycycline-inducible Cas9 into cultures from our biobank. This allows for temporally controlled target gene ablation in patient-derived cells with known growth characteristics. As proof-of-concept, we describe the derivation of clonal Cas9-inducible cells in the cell lines U3013MG (proneural, bulk forming) and U3180MG (classical, diffuse-growing). The Cas9 induction and editing efficiency was evaluated by ablation of the gene encoding the cell surface marker CD44, for which we transduced the Cas9-inducible clones with CD44 dual sgRNA vector and treated then with doxycycline over time, evaluating CD44 knockout by longitudinal flow cytometry. From a library of 106 clones, we identified the best performing clones, as evaluated by CD44 loss at day 21. Ten out of 64 clones assessed, showed potent Cas9 activity, estimating a drop in CD44 levels by 40-60% after 21 days of doxycycline treatment. The amount of editing by inducible Cas9 was higher with CD44 sgRNA administered by lentivirus than by electroporation. To ensure that the Cas9-inducible patient-derived cell lines have reproducible tumor phenotypes and did not divert from their parental growth pattern, they were transplanted orthotopically into athymic nude mice. We also validated the activity of Cas9ind in vivo by checking the editing of CD44 expression in one of our clones. The established procedure provides a basis for large-scale single-gene and pooled in vivo CRISPR studies of IDH wildtype glioblastomas with distinct invasive characteristics.
CNSC-16. MOLECULAR PROFILING AND ACTIONABLE MUTATIONS IN ADULT PATIENTS WITH IDH WILD TYPE GLIOMAS AND GLIONEURONAL AND NEURONAL TUMORS
Authors: Alessia Pellerino, Elena Maria Marchesani, Luca Bertero, Alessia Andrea Ricci, Luca Mangherini, Francesco Bruno, Riccardo Soffietti, Roberta Rudà
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Next generation sequencing (NGS) assays enable the identification of genetic alterations that may guide a personalized treatment in glioma patients. Material and METHODS From July 2021 to May 2023 a NGS analysis (Myriapod® NGS Cancer DNA and RNA panels) was performed in a cohort of 211 adults IDH wild type (wt) gliomas or circumscribed astrocytoma or glioneuronal/neuronal tumors. The aim was to identify actionable molecular alterations and provide targeted therapy at recurrence accordingly. RESULTS NGS analysis was available in 211 patients (95.5%), while NGS was not feasible in 10 patients (4.5%). 188/211 (89.1%) had an IDH wt glioblastoma (GBM) (median age 61 years), 6 (2.8%) had IDH wt lower grade gliomas (LGG) (median age 63 years), and 17 (8.1%) had circumscribed astrocytoma or glioneuronal/neuronal tumor (median age 37 years). Overall, actionable molecular alterations were found in 13/211 patients (6.2%). 7/211 patients (3.3%) had BRAF V600E mutation (3 IDH wt GBM, 1 IDH wt LGG, and 3 circumscribed/glioneuronal and neuronal tumor), 4/211 patients (1.9%) had FGFR3-TACC3 fusion (all GBM), 1/211 patients (0.5%) had PIK3CA mutation (GBM), and 1/211 patients (0.5%) had NTRK1 fusion (glioneuronal tumor). Other molecular mutations, including ALK, ERBB2, MET, KIT, KRAS, PDGFRA, and RET have not been detected. Three patients recurred after first-line therapy: 1 with BRAF mutated GBM, 1 with GBM harboring FGFR3-TACC3 fusion, and 1 with NTRK1 fusion positive glioneuronal tumor received specific BRAF/MEK inhibitor (dabrafenib/trametinib), FGFR inhibitor (pemigatinib), and NTRK inhibitor (larotrectinib), respectively. A remarkable activity of BRAF/MEK and NTRK inhibitors was observed (9 and 6 months, respectively *), while FGFR inhibitor did not display an activity to control disease (9 weeks). * ongoing CONCLUSION The incidence of actionable molecular alterations in IDH wt gliomas and glioneuronal/neuronal tumors was low. However, the use of targeted therapies may lead to significant impact on the outcome.
EXTH-57. THE IGF-2 SIGNALING PATHWAY IS A PROMISING MENINGIOMA TREATMENT TARGET
Authors: Erik Uhlmann, Rosalia Rabinovsky, Charles Mackel, Evgeny Deforzh, Rafael Vega, Hemant Varma, Anna Krichevsky
Journal: Neuro-Oncology (2023)

Abstract Meningioma is the most common primary central nervous system tumor often causing serious complications while there is no effective medical treatment. We developed a tumor-derived primary culture model featuring tumor cells with retained PDG2S lineage marker as well as non-arachnoid cells mimicking the tumor cell microenvironment. We used this model to test the relevance of miRNA differentially expressed in meningioma tumor samples identified by small RNA sequencing. We found that in all meningiomas studied, there was activation of the IGF2/miR-483 locus with high expression of both miR-483-5p and IGF2. Inhibition of miR-483-5p reduced the growth of cultured meningioma cells, whereas a miR-483 mimic increased cell proliferation. Anti-IGF2 neutralizing antibodies reduced meningioma cell proliferation. Small molecule tyrosine kinase inhibitor blockade of the IGF2 receptor (IGF1R) resulted in rapid loss of viability of cultured meningioma tumor-derived cells. Autocrine IGF2 feed-back appears to be obligatory for meningioma tumor cell survival and growth. Inhibition of this circuit with IGF1R small molecule tyrosine kinase inhibitors or receptor-binding antibodies as well as anti-IGF2 neutralizing antibodies may have therapeutic potential for meningioma.
IMMU-44. CIRCULATING CELL-FREE DNA DIRECTLY INHIBITS T CELL FUNCTION AND CONTRIBUTES TO PERIPHERAL IMMUNOSUPPRESSION IN EXPERIMENTAL GBM
Authors: Katayoun Ayasoufi, Delaney Wolf, Rachael Reesman, Frances Rangel, Lauren Gulbicki, Zachariah Tritz, Fang Jin, Michael Hansen, Cori Fain, Christian Pfaller, Aaron Johnson
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) is aggressive form of brain cancer that is associated with severe peripheral immunosuppression. This immunosuppression is a critical barrier to patient survival and the success of immunotherapies. Immunocompetent mice harboring intracranial gliomas present with the hallmark features of peripheral immunosuppression observed in GBM patients, including T cell lymphopenia. Using parabiosis, we determined that T cell lymphopenia can be transferred from glioma-bearing to healthy mice via circulation This led to the identification of a high molecular weight immunosuppressive factor in sera of glioma-bearing mice that inhibits T cell proliferation ex vivo. Proteomics analysis identified 119 proteins uniquely upregulated in the sera of glioma-bearing mice compared to controls. These proteins are associated with pathways involved in DNA response elements, cell death, and DNA-histone complexes which imply DNA release. Additional analysis revealed serum isolated from glioma-bearing mice harbor significantly higher concentrations of double stranded cell free DNA (cfDNA) compared to controls. Reducing DNA content using DNase partially reverses the proliferation defects observed in T cells when exposed to serum of glioma-bearing mice. This is while, addition of cfDNA purified from serum of glioma-bearing mice, but not genomic DNA, potently inhibited T cell function. These results were AIM2 independent implicating a novel pathway of cfDNA sensing in T cells. We contend that cfDNA induces immunosuppressive effects in experimental GBM. Devising strategies to reduce circulating cfDNA is therefore a therapeutic approach that could improve outcomes in GBM patients.
EPID-22. AN INTEGRATED, MULTI-DATABASE ANALYSIS OF THE SAFETY OF BENIGN MENINGIOMA RESECTION IN OCTOGENARIANS
Authors: Ping Zhu, Jun Ma, Clark Chen
Journal: Neuro-Oncology (2023)

Abstract OBJECT Given that multiple co-morbidities are present in up to 80% of octogenarians, resection of benign tumors, such as meningiomas, is a challenging proposition, especially in the context of frailty naturally associated with aging. Here, we characterized the patterns of clinical practice, morbidity, and mortality associated with benign meningioma resection for octogenarian using the Surveillance, Epidemiology and End RESULTS (SEER), SEER-Medicare (SEER-M), National Cancer Database (NCDB), and National Readmission Database (NRD). METHODS Logistic regression, propensity-score matching (PSM)-method (covariates balanced using PSM: socio-demographics, facility features, and comorbidities), and accelerated failure time (AFT) models. RESULTS In SEER, the adjusted odds ratios of recommendation for surgery were 0.59 (95%CI=0.53-0.66, p&amp;lt; 0.001) and 0.17 (95%CI=0.15-0.21, p&amp;lt; 0.001) for benign meningioma patients age 60-79 and &amp;gt; 80, relative to patients age 40-59. Expectedly, the hazard of death increased with advancing aging strata in patients who underwent meningioma resection. However, in independent analyses of NCDB and SEER-M, likelihood of death after benign meningioma resection was not significantly elevated in patients age &amp;gt; 80 relative to age- and PSM-matched patient cohorts. In the NRD, age &amp;gt; 80 was associated with increased odds of 90-day medical readmission after meningioma resection (OR: 1.63, 95%CI=1.33-1.99) but not 90-day neurologic readmission (OR: 1.02, 95%CI:0.76-1.37) relative to age 40-59. CONCLUSION We found no increased risk for patients age &amp;gt; 80 who were selected for and underwent resection in terms of mortality and 90-day neurologic readmission risk. However, the octogenarians have a higher risk of 90-day medical readmission. These findings suggest that neurosurgeons, in general, exert sound judgment in the selection of elderly patients for benign meningioma resections.
EPCO-51. FUNCTIONAL ANALYSIS OF REGULATORY MUTATIONS IN PEDIATRIC BRAIN TUMORS
Authors: Kiran Narta, Theodore Verhey, Varsha Thoppey Manoharan, Sorana Morrissy
Journal: Neuro-Oncology (2023)

Abstract Pediatric brain tumors are the primary cause of cancer related mortality in children and are characterized by low mutations burden. The known somatic drivers reside in the coding regions of the genome. The role of non-coding mutations in brain tumors is important yet underexplored. In this study we investigate the impact of regulatory region mutations in pediatric brain tumors. We studied 1.3 million open chromatin regions (OCRs) genome-wide from 9 studies including developing/adult brain, and cancer. Within these OCRs we identified recurring mutations in whole genome sequences from 1003 pediatric brain tumors from CBTN and PCAWG cohorts. A total of 567 OCRs with significantly recurring mutations were found, showing enrichment in brain-specific enhancers and in repressed polycomb regions in stem cells. The mutations in these OCRs resulted in motif disruption or creation of 217 transcription factor binding sites. Differential expression analysis of mutated vs nonmutated samples identified perturbations of gene or protein expression in 67 (RNA) and 16 (protein) OCR-gene pairs. Furthermore, 17 mutated OCRs were found to correlate with alterations in gene expression programs, indicating a potential regulatory role affecting multiple downstream genes. We further performed network analysis to explore clusters of OCR associated genes that share biological networks and pathways, and identified 24 clusters. Among these, OCR mutation-associated genes in 6 clusters showed a survival impact in patients. These 6 clusters mapped to pathways including mRNA decay and degradation, longevity regulating pathway, autophagy, p53 pathway, HIF2-alpha transcription factor network, pathways in cancer among others. In summary, we report functionally important regulatory elements in the genome that impact the biological processes in pediatric brain tumors.
NCMP-16. A CASE OF WIDESPREAD EXTRACRANIAL METASTASES FROM A GLIOSARCOMA
Authors: Maliheh Mohamadpour, Joshua Budhu
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND: Glioblastoma (GBM) with sarcomatous features (gliosarcoma) accounts for 2-8% of all glioblastomas1,2, characterized by a biphasic histopathology pattern consisting of glial and sarcomatous components. While GBMs generally do not metastasize outside the central nervous system (CNS), GS has been associated with extracranial metastases in up to 11% of cases3. Case presentation: A 58-year-old right-handed woman with a GBM presented to our institution for a second opinion. She was initially diagnosed 18 months prior and had received radiotherapy with concurrent temozolomide. Her adjuvant temozolomide was discontinued due to rash, and she started on bevacizumab. Her tumor progressed and she sought additional treatment options. On her initial presentation, she was tachycardic with leukocytosis, prompting admission. A chest CT showed thoracic adenopathy, multiple bilateral pulmonary nodules, and a large left malignant pleural effusion. Bronchoscopy revealed spindle cell sarcomatoid neoplasm raising the possibility of metastasis from a CNS primary tumor. Additionally, the patient endorsed development of subacute radicular pain in her bilateral lower extremities as well as weakness. MRI of total spine revealed multilevel osseous and epidural lesions, infiltrating the paraspinal muscles and thickening of cauda roots with concern for leptomeningeal disease. A subsequent PET-CT showed increased FDG avidity in these lesions. Reevaluation of the initial CNS pathology confirmed the presence of mesenchymal/sarcomatous differentiation, consistent with a diagnosis of GS. As confirmed by autopsy, the patient eventually passed away due to widespread and metastatic disease. Discussion: While GBM rarely metastasizes outside the CNS, GBM with sarcomatous features are more likely to exhibit extracranial metastasis. Our patient had widespread involvement, including the lungs, heart, liver, omentum, and bone. Metastasis was thought most likely once EBUS of the lung returned with sarcomatous features. Clinicians should therefore maintain a high suspicion for metastases when dealing with patients diagnosed with GS.
CTNI-44. NEOADJUVANT TREATMENT WITH ST101, C/EBPΒ ANTAGONIST, TRIGGERS NECROSIS AS A PATHOLOGICAL RESPONSE IN NEWLY DIAGNOSED GBM PATIENTS. TISSUE-BASED ANALYSIS FROM A SURGICAL WINDOW OF OPPORTUNITY TRIAL
Authors: Fabio Iwamoto, Abi Vainstein-Haras, Jim Rotolo, Clara Levrero, Robert Michel, Nicolas Kostelecky, Anastasia Papaioannou, Robin Buerki
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND CCAAT/enhancer-binding protein β (C/EBPβ) is a master regulator of mesenchymal transformation in GBM (Carro, 2010) and is required for maintenance of immunosuppressive tumor-associated macrophage (TAM) populations. ST101 is a first-in-class C/EBPβ antagonist, that promotes selective tumor cell death without impacting normal cell viability (Darvishi, 2022). In an ongoing phase 1/2 clinical study in rGBM (NCT04478279), ST101 administration resulted in 1 durable PR and 5 SD (range 18 to 53+ weeks). We designed a window of opportunity study to assess the effect of ST101 on clinical outcomes and pharmacodynamic biomarkers in the neoadjuvant setting in newly diagnosed GBM (ndGBM). METHODS The study will enroll 12 ndGBM patients to be treated with 2-4 500 mg ST101 IV QW) before surgical resection. After surgery, patients will continue ST101 QW + standard chemoradiation with temozolomide. RESULTS As of June 9th, 2023, 6 patients with ndGBM received 2-3 doses of ST101. MRI performed before and after neoadjuvant ST101 indicated stable disease in all patients. At surgery, however, histopathology of tumor samples showed that 4/6 patients had geographic necrosis, indicative of treatment effect after ST101 monotherapy. Evaluation of immunostaining for ST101 and molecular changes in the post-treatment tissue by bulk and single nucleus RNAseq will be conducted. CONCLUSIONS ndGBM treated with neoadjuvant ST101 monotherapy shows extensive treatment effects on the tumors that have never been treated with chemoradiation. Stability of enhancing lesions after ST101 monotherapy may not reflect the extent of treatment effect as revealed by treatment-related necrosis in the resected tissue. Analyses of the pharmacodynamics effects of ST101 on GBM cells and tumor microenvironment will be completed and presented. In addition, this study demonstrates the feasibility of a multi-institutional window of opportunity clinical trial in ndGBM patients, a decisive opportunity for determining the penetration and on-target activity of novel agents in neuro-oncology.
EXTH-76. TRANSLATIONAL BARRIERS IN 5-ALA PHOTODYNAMIC THERAPY FOR GLIOMAS: A SYSTEMATIC REVIEW OF THE IN VIVO LANDSCAPE AND FUTURE DIRECTIONS FOR CLINICAL APPLICABILITY
Authors: Debarati Bhanja, Hannah Wilding, Angel Baroz, Mara Trifoi, Ganesh Shenoy, Becky Slage-Webb, Daniel Hayes, Yasaman Soudagar, James R Connor, Alireza Mansouri
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Photodynamic therapy (PDT) is an emerging investigational therapeutic for gliomas marked by variable success. Several strategies to increase its efficacy have been attempted, and although promising, challenges that have hindered translational progress persist. The objective of this study was to analyze translational barriers through a systematic review and appraisal of the in vivo literature. Method: PRISMA guidelines were utilized to identify studies that reported translational in vivo data of 5-aminolevulinic acid (5-ALA) PDT in murine glioma models. Databases were searched from inception to 2022, using the terms: “photodynamic therapy” AND (“5-ALA” OR “ALA” OR “PPIX”) AND “in vivo” AND (“glioma” OR “glioblastoma” OR astrocytoma”). Study design parameters were appraised, and mechanistic and translational outcomes across all studies were evaluated and compared. Result: Eight studies (2002-2019) were included. The most common animal model used was immunosuppressed rats orthotopically implanted with glioma cells. Only two studies used syngeneic models. No studies validated findings in external cohorts or patient-derived xenografts. Experimental light power densities ranged widely from 0.5-100mW/ cm2. Only three studies utilized a longitudinal delivery strategy, and all found significantly decreased tumor volume and increased survival compared to high-dose single-session PDT. For mechanistic endpoints, only one study investigated the impact of PDT on the immune response, finding increased TME CD8+ T-cell infiltration in the experimental group. Safety endpoints, including hemorrhage, elevated intracranial pressure (ICP), and off-target cortical damage, were measured in only three studies, in which high power densities were associated with increased hemorrhage and elevated ICP. CONCLUSION While in vivo evidence for 5-ALA PDT is compelling, this appraisal uncovers discrepancies in power densities, lack of validation in putative translational models, and limited understanding of PDT impact on the immune response and TME. Future preclinical investigations that address these barriers will offer distinct and necessary steps toward effective clinical translation.
BIOM-63. PROTEOMIC BASED PROFILING OF CSF FOR CNSL MANAGEMENT
Authors: Aastha Aastha, Hannah Wilding, Shahbaz Khan, Nicholas Mikolajewicz, Vladimir Ignatchenko, Leonardo Jose Monteiro De Macedo Filho, Debarati Bhanja, Madison Heebner, Michael Glantz, Alireza Mansouri, Thomas Kislinger
Journal: Neuro-Oncology (2023)

Abstract Central nervous system lymphoma (CNSL) is a rare subtype of non-Hodgkin lymphoma, primarily affecting the brain and spinal cord. CNSL exhibits a dismal prognosis, as reflected by a low 5-year survival rate of 30%, with the current standard of care. The advent of multi-agent intrathecal chemotherapy (MAITC) in conjunction with systemic therapy has demonstrated encouraging outcomes, enhancing both progression-free survival and overall survival in patients with CNSL. Given the potential morbidity associated with MAITC, identification of minimally-invasive biomarkers for guiding patient management are necessary. Leveraging the longitudinal, large volume of Cerebrospinal fluid (CSF) afforded through our MAITC program, the objective of this study is to identify CSF-based proteomic biomarkers that can serve as reliable indicators of MAITC treatment response and CNSL management. Patient-matched CSF samples from the Penn State Health Neuroscience biorepository were banked at pre- and post-therapeutic endpoint in 22 primary and 36 secondary CNSL patients. The samples were profiled using high-throughput fluid sample protocol coupled with mass-spectrometry that only requires 30 μl of CSF. More than 1000 unique proteins were detected using shotgun proteomics, and 797 proteins were present in 70% of the analyzed samples, which were used for downstream analysis. We were able to effectively discriminate between primary and secondary CNSL based on protein abundance. Furthermore, the findings suggest significant changes in the cellular processes related to glycoprotein metabolism and redox signalling in response to the treatment, indicating a potential impact on protein modification and the cellular response to oxidative stress. Our comprehensive, pathway-level analysis uncovered significant molecular alterations, shedding light on their potential prognostic significance in the context of CNS lymphoma. Future work is underway to identify biomarker signatures that would predict optimal response to MAITC therapy, exhibiting potential to improve clinical decision making.